BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472566.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 196,206,618 number of mapped reads = 193,619,052 (98.68%) number of supplementary alignments = 107,889 (0.05%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 97,068,486 number of mapped paired reads (second in pair) = 96,550,566 number of mapped paired reads (both in pair) = 192,918,524 number of mapped paired reads (singletons) = 700,528 number of mapped bases = 17,805,341,603 bp number of sequenced bases = 17,802,342,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,926,275 duplication rate = 45.69% >>>>>>> Insert size mean insert size = 5,466.4485 std insert size = 709,547.032 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 51.8269 >>>>>>> ACTG content number of A's = 4,342,128,134 bp (24.39%) number of C's = 4,584,007,081 bp (25.75%) number of T's = 4,448,085,093 bp (24.99%) number of G's = 4,425,890,402 bp (24.86%) number of N's = 2,231,992 bp (0.01%) GC percentage = 50.61% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 90,699,340 number of insertions = 1,058,643 mapped reads with insertion percentage = 0.53% number of deletions = 1,311,807 mapped reads with deletion percentage = 0.66% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 5.7516X std coverageData = 54.1142X There is a 57.5% of reference with a coverageData >= 1X There is a 41.76% of reference with a coverageData >= 2X There is a 27.07% of reference with a coverageData >= 3X There is a 19.89% of reference with a coverageData >= 4X There is a 13.88% of reference with a coverageData >= 5X There is a 10.79% of reference with a coverageData >= 6X There is a 8.42% of reference with a coverageData >= 7X There is a 7.11% of reference with a coverageData >= 8X There is a 6.15% of reference with a coverageData >= 9X There is a 5.56% of reference with a coverageData >= 10X There is a 5.13% of reference with a coverageData >= 11X There is a 4.83% of reference with a coverageData >= 12X There is a 4.6% of reference with a coverageData >= 13X There is a 4.42% of reference with a coverageData >= 14X There is a 4.26% of reference with a coverageData >= 15X There is a 4.13% of reference with a coverageData >= 16X There is a 4.02% of reference with a coverageData >= 17X There is a 3.91% of reference with a coverageData >= 18X There is a 3.82% of reference with a coverageData >= 19X There is a 3.73% of reference with a coverageData >= 20X There is a 3.65% of reference with a coverageData >= 21X There is a 3.58% of reference with a coverageData >= 22X There is a 3.5% of reference with a coverageData >= 23X There is a 3.44% of reference with a coverageData >= 24X There is a 3.37% of reference with a coverageData >= 25X There is a 3.31% of reference with a coverageData >= 26X There is a 3.25% of reference with a coverageData >= 27X There is a 3.2% of reference with a coverageData >= 28X There is a 3.14% of reference with a coverageData >= 29X There is a 3.09% of reference with a coverageData >= 30X There is a 3.04% of reference with a coverageData >= 31X There is a 2.99% of reference with a coverageData >= 32X There is a 2.94% of reference with a coverageData >= 33X There is a 2.9% of reference with a coverageData >= 34X There is a 2.85% of reference with a coverageData >= 35X There is a 2.81% of reference with a coverageData >= 36X There is a 2.76% of reference with a coverageData >= 37X There is a 2.72% of reference with a coverageData >= 38X There is a 2.68% of reference with a coverageData >= 39X There is a 2.64% of reference with a coverageData >= 40X There is a 2.61% of reference with a coverageData >= 41X There is a 2.57% of reference with a coverageData >= 42X There is a 2.53% of reference with a coverageData >= 43X There is a 2.49% of reference with a coverageData >= 44X There is a 2.46% of reference with a coverageData >= 45X There is a 2.42% of reference with a coverageData >= 46X There is a 2.39% of reference with a coverageData >= 47X There is a 2.36% of reference with a coverageData >= 48X There is a 2.32% of reference with a coverageData >= 49X There is a 2.29% of reference with a coverageData >= 50X There is a 2.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1745612599 7.003443329435075 46.19567563598746 chr2 243199373 1212717014 4.986513735789935 38.99888944957031 chr3 198022430 946752278 4.781035552386666 28.254973103097672 chr4 191154276 744780512 3.896227317457445 30.747526911411374 chr5 180915260 888700058 4.912244870885961 42.717174970887214 chr6 171115067 822501619 4.806716517838841 26.433438726543 chr7 159138663 1137800971 7.149745696933498 156.3563833862673 chr8 146364022 941058059 6.429572282456135 100.99734609449013 chr9 141213431 791304008 5.6036030170529605 32.71932361612401 chr10 135534747 733545960 5.412235432143463 32.5597846364321 chr11 135006516 912889572 6.761818607332997 34.391362553398174 chr12 133851895 774180493 5.783859040620979 27.57576402337435 chr13 115169878 346829838 3.011463101489089 16.780125784586883 chr14 107349540 482803374 4.497488987842892 24.973197160136813 chr15 102531392 742204467 7.238802209961219 41.37092420656927 chr16 90354753 791911315 8.764467708743556 43.2306641362297 chr17 81195210 911409782 11.224920558737393 57.77707006185584 chr18 78077248 311923138 3.995058048152517 30.965914655551426 chr19 59128983 910777539 15.403233622333738 57.2215700750356 chr20 63025520 412912895 6.5515190513303185 38.439070085314576 chr21 48129895 228400357 4.7454987591392 36.50747296783859 chr22 51304566 449721667 8.76572402931934 51.152559991896254 chrMT 16571 14443455 871.6103433709493 214.04540327802422 chrX 155270560 404091971 2.6025021807095947 14.75291642845581 chrY 59373566 146068662 2.4601631978783285 40.6740804553005